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Translation in E. coli is initiated at the start ATG codon, which encodes for the amino acid Methionine (Met). In some cases, the start codon can be GTG, which within the open reading frame (ORF) would encode for Valine (Val). If it is in the start of the ORF, does a tRNA loaded with Met get selected? The frequency this codon is used as a start codon is 15%. How would this affect the efficiency of initiation of translation?

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up vote 7 down vote accepted

The NCBI translation table translates all alternative start sites as methionines. To my understanding, all translation is initiated by the fMet-tRNA. I don't know if there are any exceptions to this rule.

Regarding translation efficiency, I only found a 1985 paper in PNAS (Reddy et al, PNAS 82:5656-60), in which they compared the translation efficiency of adenilate cyclase's own UUG start vs GUG or AUG, obtaining a translation ratio 1:2:6 UUG:GUG:AUG, suggesting that AUG is the most efficient one, followed by GUG. Also, Romero and Garcia, FEMS microbiology letters 84:325-330 (1991) compared the efficiency of AUG vs AUC, AUA and AUU, showing a much lower efficiency for those codons, but they did not compare it to GUG.

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